The impact of whole-genome duplications in the topology of angiosperm gene regulatory networks
VIB-UGent Center for Plant Systems Biology
WGD or poliploidy: duplication of an organism’s entire set of chromosomes.
Key source of extra genetic material for evolution to work with.
WGD events have occurred in multiple taxa, e.g.:
WGD have contributed to:
Survival and establishment of polyploids is challenging.
Detrimental effects of WGD include:
Surviving polyploids undergo a rediploidization process that leads to genome fractionation (i.e., loss of functional DNA sequences).
Preferential retention of genes encoding proteins involved in intricately connected systems, e.g.:
The gene balance hypothesis: preservation of stoichiometric balance explains the biased retention.
Using TFs to study the impact of genome duplications.
TF activity can be explored globally in gene regulatory networks (GRNs).
Network motifs are genetic circuits that have been positively selected.
Gene and genome duplications can create novel motifs.
Data source:
Enrichment of WGD-derived genes in the PPI networks of all species (P < 0.001).
WGD-derived genes in PPI networks are enriched in dosage sensitive processes, e.g.:
Conclusion
Our findings agree with the gene balance hypothesis - association between WGD and protein-protein interaction.
Conclusion
Dosage balance imposes selective pressures that constrain sequence divergence in interacting WGD-derived genes.
Measuring interaction similarity:
\[ S(A,B) = \frac{2 \left| A \cap B \right|}{ \left|A \right| + \left| B \right|} \]
WGD-derived pairs have higher interaction similarity than SSD-derived pairs.
The difference is more pronounced for older pairs.
Measuring interaction similarity:
\[ S(A,B) = \frac{2 \left| A \cap B \right|}{ \left|A \right| + \left| B \right|} \]
WGD-derived pairs have higher interaction similarity than SSD-derived pairs.
The difference is more pronounced for older pairs.
Conclusion
Dosage balance imposes selective pressures that prevent ohnologs from losing and gaining interactions.
Genes from recent WGD are more frequently part of motifs than genes from ancient WGD.
WGD-derived motifs are quickly lost over time (fractionation or rewiring?)
Species with recent WGD events generally have higher motif frequencies, regardless of the duplication mode that created the genes forming motifs.
Species with recent WGD events generally have higher motif frequencies, regardless of the duplication mode that created the genes forming motifs.
Conclusion
WGD events have a more significant impact on the short-term evolution of polyploids.
This explains associations between WGD events and surviving environmental turmoil (e.g., the Cretaceous-Paleogene extinction and glaciation events).
Functional enrichment of GO terms, InterPro domains, and TF families.
WGD: growth and development, especially dosage dependent-processes, e.g.:
SSD: response to stress and environmental stimuli, e.g.:
Functional enrichment of GO terms, InterPro domains, and TF families.
WGD: growth and development, especially dosage dependent-processes, e.g.:
SSD: response to stress and environmental stimuli, e.g.:
Conclusion
The patterns observed for WGD- and SSD-derived motifs are very similar to what has been observed for WGD- and SSD-derived genes.
Dosage balance imposes selective constraints to WGD-derived genes that lead to:
WGD has a more significant impact in the short-term evolution of polyploids, but WGD-derived motifs are lost over time.
WGD contributes to GRNs with genes related to growth and development, while SSD contributes with stress-related genes.
DOI: 10.1093/molbev/msad141
Dr. Yves Van de Peer (supervision)
Ghent University and ERC (funding)
VIB Center for Plant Systems Biology (infrastructure)
almeidasilvaf
almeidasilvaf
https://almeidasilvaf.github.io
Fabricio Almeida-Silva
0000-0002-5314-2964
Fabricio Almeida-Silva @almeidasilvaf